DL_FFLUX Refactored: Accelerating Quantum Chemical Topology Simulations With Optimized Parallelization

IF 2.9 3区 化学 Q2 CHEMISTRY, MULTIDISCIPLINARY
Mohamadhosein Nosratjoo, Michael K. Bane, Paul L. A. Popelier
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引用次数: 0

Abstract

Molecular dynamics simulations are only as useful as they are both accurate and efficient. Here, we introduce an upgraded version of the simulation code DL_FFLUX that dramatically extends accessible time scales by combining a more efficient core algorithm with OpenMP and MPI parallelization. DL_FFLUX is a unique, state-of-the-art polarisable machine learning potential (MLP) that combines Quantum Chemical Topology (QCT) and machine learning (ML) and relies on DL_POLY as the driver for molecular dynamics simulations. This new implementation of DL_FFLUX delivers a massive performance boost, making simulations 6.8 to 49 times faster without compromising accuracy. This performance boost of DL_FFLUX is reported for condensed-phase simulations of water and ethanol and for single-molecule simulations of 6 small to medium-sized molecules. Moreover, we compared the optimized version of DL_FFLUX with other MLPs on the MD17 dataset for four molecules. DL_FFLUX is the fastest: depending on the system, it outperforms the second-fastest MLP by a factor of 1.8–9.6.

DL_FFLUX重构:加速量子化学拓扑模拟与优化并行
分子动力学模拟只有在既准确又高效的情况下才有用。在这里,我们介绍了仿真代码DL_FFLUX的升级版本,通过将更高效的核心算法与OpenMP和MPI并行化相结合,极大地扩展了可访问的时间尺度。DL_FFLUX是一种独特的、最先进的极化机器学习潜力(MLP),它结合了量子化学拓扑(QCT)和机器学习(ML),并依赖于DL_POLY作为分子动力学模拟的驱动程序。这个新实现的DL_FFLUX提供了巨大的性能提升,使模拟速度提高6.8到49倍,而不影响准确性。据报道,DL_FFLUX的性能提升适用于水和乙醇的凝聚相模拟,以及6个中小分子的单分子模拟。此外,我们将优化后的DL_FFLUX与MD17数据集上的其他MLPs进行了比较。DL_FFLUX是最快的:根据系统的不同,它的性能比第二快的MLP高出1.8-9.6倍。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
CiteScore
6.60
自引率
3.30%
发文量
247
审稿时长
1.7 months
期刊介绍: This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
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